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Arévalo PR, Aylan B, Gutierrez MG. Quantitative Spatio-temporal Analysis of Phagosome Maturation in Live Cells. Methods Mol Biol 2023; 2692:187-207. [PMID: 37365469 DOI: 10.1007/978-1-0716-3338-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Phagocytosis and phagosome maturation are central processes to the development of the innate and adaptive immune response. Phagosome maturation is a continuous and dynamic process that occurs rapidly. In this chapter we describe fluorescence-based live cell imaging methods for the quantitative and temporal analysis of phagosome maturation of beads and M. tuberculosis as two phagocytic targets. We also describe simple protocols for monitoring phagosome maturation: the use of the acidotropic probe LysoTracker and analyzing the recruitment of EGFP-tagged host proteins by phagosomes.
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Affiliation(s)
- Patricia Rosell Arévalo
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Beren Aylan
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK.
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2
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Nakada-Tsukui K, Watanabe N, Shibata K, Wahyuni R, Miyamoto E, Nozaki T. Proteomic analysis of Atg8-dependent recruitment of phagosomal proteins in the enteric protozoan parasite Entamoeba histolytica. Front Cell Infect Microbiol 2022; 12:961645. [PMID: 36262186 PMCID: PMC9575557 DOI: 10.3389/fcimb.2022.961645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Autophagy is one of the bulk degradation systems and is conserved throughout eukaryotes. In the enteric protozoan parasite Entamoeba histolytica, the causative agent of human amebiasis, Atg8 is not exclusively involved in autophagy per se but also in other membrane traffic-related pathways such as phagosome biogenesis. We previously reported that repression of atg8 gene expression by antisense small RNA-mediated transcriptional gene silencing (gs) resulted in growth retardation, delayed endocytosis, and reduced acidification of endosomes and phagosomes. In this study, to better understand the role of Atg8 in phagocytosis and trogocytosis, we conducted a comparative proteomic analysis of phagosomes isolated from wild type and atg8-gs strains. We found that 127 and 107 proteins were detected >1.5-fold less or more abundantly, respectively, in phagosomes isolated from the atg8-gs strain, compared to the control strain. Among 127 proteins whose abundance was reduced in phagosomes from atg8-gs, a panel of proteins related to fatty acid metabolism, phagocytosis, and endoplasmic reticulum (ER) homeostasis was identified. Various lysosomal hydrolases and their receptors also tend to be excluded from phagosomes by atg8-gs, reinforcing the notion that Atg8 is involved in phagosomal acidification and digestion. On the contrary, among 107 proteins whose abundance increased in phagosomes from atg8-gs strain, ribosome-related proteins and metabolite interconversion enzymes are enriched. We further investigated the localization of several representative proteins, including adenylyl cyclase-associated protein and plasma membrane calcium pump, both of which were demonstrated to be recruited to phagosomes and trogosomes via an Atg8-dependent mechanism. Taken together, our study has provided the basis of the phagosome proteome to further elucidate molecular events in the Atg8-dependent regulatory network of phagosome/trogosome biogenesis in E. histolytica.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Kumiko Nakada-Tsukui, ; Tomoyoshi Nozaki,
| | - Natsuki Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kumiko Shibata
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ratna Wahyuni
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Miyamoto
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- *Correspondence: Kumiko Nakada-Tsukui, ; Tomoyoshi Nozaki,
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3
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Sui L, Guo HC. Enhanced recombinant expression and purification of human IRAP for biochemical and crystallography studies. Biochem Biophys Rep 2021; 27:101042. [PMID: 34169156 PMCID: PMC8207215 DOI: 10.1016/j.bbrep.2021.101042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Insulin-regulated aminopeptidase (IRAP) in humans is a membrane bound enzyme that has multiple functions. It was first described as a companion protein of the insulin-responsive glucose transporter, Glut4, in specialized vesicles. The protein has subsequently been shown to be identical to the oxytocinase/aminopeptidase or the angiotensin IV (Ang IV) receptor (AT4 receptor). Some AT4 ligand peptides, such as Ang IV and LVV-hemorphin-7, have been shown to act as IRAP inhibitors that exert memory-enhancing properties. As such IRAP has been a target for developing cognitive enhancers. To facilitate detailed mechanistic studies of IRAP catalysis and inhibition, and to pave the way for biophysical and structural studies of IRAP in complex with peptide inhibitors, we report here an optimized expression and purification system using High Five insect cells. We also report biochemical characterizations of the purified recombinant IRAP with a standard aminopeptidase substrate and an optimized IRAP peptide inhibitor with a Ki of 98 nM.
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Key Words
- AT4, Ang IV receptor
- Ang IV, angiotensin IV
- Cognitive enhancers
- Crystallization
- ERAP, endoplasmic reticulum aminopeptidase
- Expression and purification
- IEX, ion exchange chromatography
- IMAC, immobilized metal ion affinity chromatography
- IRAP, insulin-regulated aminopeptidase
- Insulin-regulated aminopeptidase (IRAP)
- L-AMC, leucine 7-amido-4-methylcoumarin
- LVV-H7, LVV-hemorphin-7
- MHC-I, major histocompatibility complex class I
- Peptide inhibitor
- SEC, size exclusion chromatography
- Substrate affinity
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Affiliation(s)
- Lufei Sui
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA, 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA, 01854, USA
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4
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Dziurdzik SK, Conibear E. The Vps13 Family of Lipid Transporters and Its Role at Membrane Contact Sites. Int J Mol Sci 2021; 22:ijms22062905. [PMID: 33809364 PMCID: PMC7999203 DOI: 10.3390/ijms22062905] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/27/2022] Open
Abstract
The conserved VPS13 proteins constitute a new family of lipid transporters at membrane contact sites. These large proteins are suspected to bridge membranes and form a direct channel for lipid transport between organelles. Mutations in the 4 human homologs (VPS13A–D) are associated with a number of neurological disorders, but little is known about their precise functions or the relevant contact sites affected in disease. In contrast, yeast has a single Vps13 protein which is recruited to multiple organelles and contact sites. The yeast model system has proved useful for studying the function of Vps13 at different organelles and identifying the localization determinants responsible for its membrane targeting. In this review we describe recent advances in our understanding of VPS13 proteins with a focus on yeast research.
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Affiliation(s)
- Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Correspondence:
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5
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Nguyen JA, Yates RM. Better Together: Current Insights Into Phagosome-Lysosome Fusion. Front Immunol 2021; 12:636078. [PMID: 33717183 PMCID: PMC7946854 DOI: 10.3389/fimmu.2021.636078] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Following phagocytosis, the nascent phagosome undergoes maturation to become a phagolysosome with an acidic, hydrolytic, and often oxidative lumen that can efficiently kill and digest engulfed microbes, cells, and debris. The fusion of phagosomes with lysosomes is a principal driver of phagosomal maturation and is targeted by several adapted intracellular pathogens. Impairment of this process has significant consequences for microbial infection, tissue inflammation, the onset of adaptive immunity, and disease. Given the importance of phagosome-lysosome fusion to phagocyte function and the many virulence factors that target it, it is unsurprising that multiple molecular pathways have evolved to mediate this essential process. While the full range of these pathways has yet to be fully characterized, several pathways involving proteins such as members of the Rab GTPases, tethering factors and SNAREs have been identified. Here, we summarize the current state of knowledge to clarify the ambiguities in the field and construct a more comprehensive phagolysosome formation model. Lastly, we discuss how other cellular pathways help support phagolysosome biogenesis and, consequently, phagocyte function.
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Affiliation(s)
- Jenny A Nguyen
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Robin M Yates
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, Snyder Institute of Chronic Disease, University of Calgary, Calgary, AB, Canada
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6
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Levin-Konigsberg R, Mantegazza AR. A guide to measuring phagosomal dynamics. FEBS J 2020; 288:1412-1433. [PMID: 32757358 PMCID: PMC7984381 DOI: 10.1111/febs.15506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/07/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
Phagocytosis is an essential mechanism for immunity and homeostasis, performed by a subset of cells known as phagocytes. Upon target engulfment, de novo formation of specialized compartments termed phagosomes takes place. Phagosomes then undergo a series of fusion and fission events as they interact with the endolysosomal system and other organelles, in a dynamic process known as phagosome maturation. Because phagocytes play a key role in tissue patrolling and immune surveillance, phagosome maturation is associated with signaling pathways that link phagocytosis to antigen presentation and the development of adaptive immune responses. In addition, and depending on the nature of the cargo, phagosome integrity may be compromised, triggering additional cellular mechanisms including inflammation and autophagy. Upon completion of maturation, phagosomes enter a recently described phase: phagosome resolution, where catabolites from degraded cargo are metabolized, phagosomes are resorbed, and vesicles of phagosomal origin are recycled. Finally, phagocytes return to homeostasis and become ready for a new round of phagocytosis. Altogether, phagosome maturation and resolution encompass a series of dynamic events and organelle crosstalk that can be measured by biochemical, imaging, photoluminescence, cytometric, and immune‐based assays that will be described in this guide.
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Affiliation(s)
| | - Adriana R Mantegazza
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Mao F, Mu H, Wong NK, Liu K, Song J, Qiu J, Lin Y, Zhang X, Xu D, Xiang Z, Li J, Zhang Y, Yu Z. Hemocyte phagosomal proteome is dynamically shaped by cytoskeleton remodeling and interorganellar communication with endoplasmic reticulum during phagocytosis in a marine invertebrate, Crassostrea gigas. Sci Rep 2020; 10:6577. [PMID: 32313134 PMCID: PMC7171069 DOI: 10.1038/s41598-020-63676-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
Phagosomes are task-force organelles of innate immune systems, and evolutionary diversity and continuity abound in the protein machinery executing this coordinately regulated process. In order to clarify molecular mechanisms underlying phagocytosis, we studied phagocyte response to beads and Vibrio species, using hemocytes of the Pacific oysters (Crassostrea gigas) as a marine invertebrate model. Phagosomes from different stages of phagocytosis were isolated by density-gradient centrifugation, and more than 400 phagosome-associated proteins were subsequently identified via high-throughput quantitative proteomics. In modeling key networks of phagosomal proteins, our results support the essential roles of several processes driving phagosome formation and maturation, including cytoskeleton remodeling and signal transduction by Rab proteins. Several endoplasmic reticulum (ER)-associated proteins were identified, while live cell imaging confirms an apparent intimate interaction between the ER and phagosomes. In further quantitative proteomic analysis, the signal transducers CgRhoGDI and CgPI4K were implicated. Through experimental validation, CgRhoGDI was shown to negatively regulate actin cytoskeleton remodeling in the formation of oyster phagosomes, while CgPI4K signaling drives phagosome maturation and bacterial killing. Our current work illustrates the diversity and dynamic interplay of phagosomal proteins, providing a framework for better understanding host-microbe interactions during phagosome activities in under-examined invertebrate species.
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Affiliation(s)
- Fan Mao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Huawei Mu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Nai-Kei Wong
- Department of Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Kunna Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jingchen Song
- College of Oceanology, South China Agricultural University, Guangzhou, China
| | - Jianwen Qiu
- Croucher Institute for Environmental Sciences and the Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yue Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xiangyu Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Duo Xu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhiming Xiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China. .,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
| | - Ziniu Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China. .,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
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8
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Coppens I, Romano JD. Sitting in the driver's seat: Manipulation of mammalian cell Rab GTPase functions by apicomplexan parasites. Biol Cell 2020; 112:187-195. [DOI: 10.1111/boc.201900107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Isabelle Coppens
- Department of Molecular Microbiology and Immunology Johns Hopkins University Bloomberg School of Public Health Baltimore MD 21205 USA
| | - Julia D. Romano
- Department of Molecular Microbiology and Immunology Johns Hopkins University Bloomberg School of Public Health Baltimore MD 21205 USA
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9
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Levin‐Konigsberg R, Grinstein S. Phagosome‐endoplasmic reticulum contacts: Kissing and not running. Traffic 2019; 21:172-180. [DOI: 10.1111/tra.12708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022]
Affiliation(s)
| | - Sergio Grinstein
- Division of Cell BiologyHospital for Sick Children Toronto Ontario Canada
- Department of BiochemistryUniversity of Toronto Toronto Ontario Canada
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10
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Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E. Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation. Mol Cell Proteomics 2019; 18:909-922. [PMID: 30808727 DOI: 10.1074/mcp.ra119.001316] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/23/2019] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) are professional phagocytes that use innate sensing and phagocytosis to internalize and degrade self as well as foreign material, such as pathogenic bacteria, within phagosomes. These intracellular compartments are equipped to generate antigenic peptides that serve as source for antigen presentation to T cells initiating adaptive immune responses. The phagosomal proteome of DCs is only partially studied and is highly dynamic as it changes during phagosome maturation, when phagosomes sequentially interact with endosomes and lysosomes. In addition, the activation status of the phagocyte can modulate the phagosomal composition and is able to shape phagosomal functions.In this study, we determined spatiotemporal changes of the proteome of DC phagosomes during their maturation and compared resting and lipopolysaccharide (LPS)-stimulated bone marrow-derived DCs by label-free, quantitative mass spectrometry. Ovalbumin-coupled latex beads were used as phagocytosis model system and revealed that LPS-treated DCs show decreased recruitment of proteins involved in phagosome maturation, such as subunits of the vacuolar proton ATPase, cathepsin B, D, S, and RAB7. In contrast, those phagosomes were characterized by an increased recruitment of proteins involved in antigen cross-presentation, e.g. different subunits of MHC I molecules, the proteasome and tapasin, confirming the observed increase in cross-presentation efficacy in those cells. Further, several proteins were identified that were not previously associated with phagosomal functions. Hierarchical clustering of phagosomal proteins demonstrated that their acquisition to DC phagosomes is not only dependent on the duration of phagosome maturation but also on the activation state of DCs. Thus, our study provides a comprehensive overview of how DCs alter their phagosome composition in response to LPS, which has profound impact on the initiation of efficient immune responses.
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Affiliation(s)
- Anne-Marie Pauwels
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Anetta Härtlova
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Julien Peltier
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Yasmine Driege
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Griet Baudelet
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Priscille Brodin
- ‖Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Matthias Trost
- ¶Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rudi Beyaert
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eik Hoffmann
- From the ‡Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium;; §Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium;; ‖Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
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11
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Dingjan I, Linders PTA, Verboogen DRJ, Revelo NH, Ter Beest M, van den Bogaart G. Endosomal and Phagosomal SNAREs. Physiol Rev 2018; 98:1465-1492. [PMID: 29790818 DOI: 10.1152/physrev.00037.2017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein family is of vital importance for organelle communication. The complexing of cognate SNARE members present in both the donor and target organellar membranes drives the membrane fusion required for intracellular transport. In the endocytic route, SNARE proteins mediate trafficking between endosomes and phagosomes with other endosomes, lysosomes, the Golgi apparatus, the plasma membrane, and the endoplasmic reticulum. The goal of this review is to provide an overview of the SNAREs involved in endosomal and phagosomal trafficking. Of the 38 SNAREs present in humans, 30 have been identified at endosomes and/or phagosomes. Many of these SNAREs are targeted by viruses and intracellular pathogens, which thereby reroute intracellular transport for gaining access to nutrients, preventing their degradation, and avoiding their detection by the immune system. A fascinating picture is emerging of a complex transport network with multiple SNAREs being involved in consecutive trafficking routes.
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Affiliation(s)
- Ilse Dingjan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Peter T A Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Danielle R J Verboogen
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Natalia H Revelo
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen , The Netherlands ; and Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen , The Netherlands
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12
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Müller GDAES, Lüchmann KH, Razzera G, Toledo-Silva G, Bebianno MJ, Marques MRF, Bainy ACD. Proteomic response of gill microsomes of Crassostrea brasiliana exposed to diesel fuel water-accommodated fraction. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 201:109-118. [PMID: 29906693 DOI: 10.1016/j.aquatox.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 05/28/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Diesel fuel water-accommodated fraction (diesel-WAF) is a complex mixture of organic compounds that may cause harmful effects to marine invertebrates. Expression of microsomal proteins can be changed by oil exposure, causing functional alterations in endoplasmic reticulum (ER). The aim of this study was to investigate changes in protein expression signatures in microsomes of oysterl Crassostrea brasiliana (=C.gasar) gill after exposure to 10% diesel-WAF for 24 and 72 h. Protein expression signatures of gills of oysters exposed to diesel-WAF were compared to those of unexposed oysters using two-dimensional electrophoresis (2-DE) to identify differentially expressed proteins. A total of 458 protein spots with molecular weights between 30-75 kDa were detected by 2-DE in six replicates of exposed oyster proteomes compared to unexposed ones. Fourteen differentially expressed proteins (six up-regulated and eight down-regulated) were identified. They are: proteins related to xenobiotic biotransformation (cytochrome P450 6 A, NADPH-cytochrome P450 reductase); cytoskeleton (α-tubulin, β-tubulin, gelsolin); processing and degradation of proteins pathways (thioredoxin domain-containing protein E3 ubiquitin-protein ligase MIB2); involved in the biosynthesis of glycolipids and glycoproteins (beta-1,3-galactosyltransferase 1); associated with stress responses (glutamate receptor 4 and 14-3-3 protein zeta, corticotropin-releasing factor-binding protein); plasmalogen biosynthesis (fatty acyl-CoA reductase 1), and sodium-and chloride-dependent glycine transporter 2 and glyoxylate reductase/hydroxypyruvate reductase. Different patterns of protein responses were observed between 24 and 72 h-exposed groups. Expression pattern of microsomal proteins provided a first insight on the potential diesel-WAF effects at protein level in microsomal fraction of oyster gills and indicated new potential biomarkers of exposure and effect. The present work can be a basis for future ecotoxicological studies in oysters aiming to elucidate the molecular mechanisms behind diesel-WAF toxicity and for environmental monitoring programs.
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Affiliation(s)
- Gabrielle do Amaral E Silva Müller
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Karim Hahn Lüchmann
- Laboratory of Biochemistry and Molecular Biology - LBBM, Fishery Engineering Department, Santa Catarina State University, Laguna, 88790-000, Brazil
| | - Guilherme Razzera
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Guilherme Toledo-Silva
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Maria João Bebianno
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; Centre of Marine and Environmental Research (CIMA), University of Algarve, Campus de Gambelas, 8000-139 Faro, Portugal
| | - Maria Risoleta Freire Marques
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Afonso Celso Dias Bainy
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil.
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13
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Schmidt H, Vlaic S, Krüger T, Schmidt F, Balkenhol J, Dandekar T, Guthke R, Kniemeyer O, Heinekamp T, Brakhage AA. Proteomics of Aspergillus fumigatus Conidia-containing Phagolysosomes Identifies Processes Governing Immune Evasion. Mol Cell Proteomics 2018; 17:1084-1096. [PMID: 29507050 DOI: 10.1074/mcp.ra117.000069] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 02/17/2018] [Indexed: 12/12/2022] Open
Abstract
Invasive infections by the human pathogenic fungus Aspergillus fumigatus start with the outgrowth of asexual, airborne spores (conidia) into the lung tissue of immunocompromised patients. The resident alveolar macrophages phagocytose conidia, which end up in phagolysosomes. However, A. fumigatus conidia resist phagocytic degradation to a certain degree. This is mainly attributable to the pigment 1,8-dihydroxynaphthalene (DHN) melanin located in the cell wall of conidia, which manipulates the phagolysosomal maturation and prevents their intracellular killing. To get insight in the underlying molecular mechanisms, we comparatively analyzed proteins of mouse macrophage phagolysosomes containing melanized wild-type (wt) or nonmelanized pksP mutant conidia. For this purpose, a protocol to isolate conidia-containing phagolysosomes was established and a reference protein map of phagolysosomes was generated. We identified 637 host and 22 A. fumigatus proteins that were differentially abundant in the phagolysosome. 472 of the host proteins were overrepresented in the pksP mutant and 165 in the wt conidia-containing phagolysosome. Eight of the fungal proteins were produced only in pksP mutant and 14 proteins in wt conidia-containing phagolysosomes. Bioinformatical analysis compiled a regulatory module, which indicates host processes affected by the fungus. These processes include vATPase-driven phagolysosomal acidification, Rab5 and Vamp8-dependent endocytic trafficking, signaling pathways, as well as recruitment of the Lamp1 phagolysosomal maturation marker and the lysosomal cysteine protease cathepsin Z. Western blotting and immunofluorescence analyses confirmed the proteome data and moreover showed differential abundance of the major metabolic regulator mTOR. Taken together, with the help of a protocol optimized to isolate A. fumigatus conidia-containing phagolysosomes and a potent bioinformatics algorithm, we were able to confirm A. fumigatus conidia-dependent modification of phagolysosomal processes that have been described before and beyond that, identify pathways that have not been implicated in A. fumigatus evasion strategy, yet.Mass spectrometry proteomics data are available via ProteomeXchange with identifiers PXD005724 and PXD006134.
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Affiliation(s)
- Hella Schmidt
- From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Sebastian Vlaic
- §Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Thomas Krüger
- From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Franziska Schmidt
- From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Johannes Balkenhol
- ¶Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- ¶Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Reinhard Guthke
- §Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Olaf Kniemeyer
- From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Thorsten Heinekamp
- From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany; .,‖Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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14
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Zheng YZ, DeMarco ML. Manipulating trypsin digestion conditions to accelerate proteolysis and simplify digestion workflows in development of protein mass spectrometric assays for the clinical laboratory. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2017; 6:1-12. [PMID: 39193414 PMCID: PMC11322774 DOI: 10.1016/j.clinms.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 10/09/2017] [Accepted: 10/17/2017] [Indexed: 01/15/2023]
Abstract
For ease of measurement and accurate identification of proteins by mass spectrometry, protein targets are commonly cleaved into peptides. Protein digestion is a critical step in sample preparation, yielding peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity; however, it can yield highly variable digestion profiles and is dependent on several factors including digestion buffer, denaturant, trypsin quality selected, and composition/complexity of the sample matrix. Historically, trypsin digestion protocols have relied on lengthy digestion times-which are unsuitable for many clinical applications-to ensure effective proteolysis. Here, we performed an iterative and comprehensive evaluation of digestion conditions for five structurally diverse proteins in plasma and serum: apolipoprotein A-1, retinol-binding protein 4, transthyretin, complement component 9 and C-reactive protein. Conditions were monitored for improvements in signal intensity, reproducibility of digestion profile, and rate of release of proteolytic peptides. This approach yielded an optimized digestion protocol for detection of all five proteins in a single workflow requiring a brief 20 min digestion, without the use of chemical denaturants or reduction/alkylation steps, and only 1 μl of plasma. It is our hope that this data can accelerate the development phase of targeted mass spectrometric protein assays by identifying practical approaches to accelerate and simplify digestion protocols for clinical applications and assist with the selection of tryptic peptides for protein quantitation.
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Affiliation(s)
- Yu Zi Zheng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Providence Health Care, Vancouver, Canada
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15
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Gutiérrez S, Wolke M, Plum G, Robinson N. Isolation of Salmonella typhimurium-containing Phagosomes from Macrophages. J Vis Exp 2017. [PMID: 29155747 DOI: 10.3791/56514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Salmonella typhimurium is a facultative intracellular bacterium that causes gastroenteritis in humans. After invasion of the lamina propria, S. typhimurium bacteria are quickly detected and phagocytized by macrophages, and contained in vesicles known as phagosomes in order to be degraded. Isolation of S. typhimurium-containing phagosomes have been widely used to study how S. typhimurium infection alters the process of phagosome maturation to prevent bacterial degradation. Classically, the isolation of bacteria-containing phagosomes has been performed by sucrose gradient centrifugation. However, this process is time-consuming, and requires specialized equipment and a certain degree of dexterity. Described here is a simple and quick method for the isolation of S. typhimurium-containing phagosomes from macrophages by coating the bacteria with biotin-streptavidin-conjugated magnetic beads. Phagosomes obtained by this method can be suspended in any buffer of choice, allowing the utilization of isolated phagosomes for a broad range of assays, such as protein, metabolite, and lipid analysis. In summary, this method for the isolation of S. typhimurium-containing phagosomes is specific, efficient, rapid, requires minimum equipment, and is more versatile than the classical method of isolation by sucrose gradient-ultracentrifugation.
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Affiliation(s)
- Saray Gutiérrez
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne; Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne
| | - Martina Wolke
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne
| | - Georg Plum
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne
| | - Nirmal Robinson
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne; Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne;
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16
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Semini G, Aebischer T. Phagosome proteomics to study Leishmania's intracellular niche in macrophages. Int J Med Microbiol 2017; 308:68-76. [PMID: 28927848 DOI: 10.1016/j.ijmm.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/23/2017] [Accepted: 09/03/2017] [Indexed: 12/14/2022] Open
Abstract
Intracellular pathogens invade their host cells and replicate within specialized compartments. In turn, the host cell initiates a defensive response trying to kill the invasive agent. As a consequence, intracellular lifestyle implies morphological and physiological changes in both pathogen and host cell. Leishmania spp. are medically important intracellular protozoan parasites that are internalized by professional phagocytes such as macrophages, and reside within the parasitophorous vacuole inhibiting their microbicidal activity. Whereas the proteome of the extracellular promastigote form and the intracellular amastigote form have been extensively studied, the constituents of Leishmania's intracellular niche, an endolysosomal compartment, are not fully deciphered. In this review we discuss protocols to purify such compartments by means of an illustrating example to highlight generally relevant considerations and innovative aspects that allow purification of not only the intracellular parasites but also the phagosomes that harbor them and analyze the latter by gel free proteomics.
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Affiliation(s)
- Geo Semini
- Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany.
| | - Toni Aebischer
- Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
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17
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Danelishvili L, Chinison JJJ, Pham T, Gupta R, Bermudez LE. The Voltage-Dependent Anion Channels (VDAC) of Mycobacterium avium phagosome are associated with bacterial survival and lipid export in macrophages. Sci Rep 2017; 7:7007. [PMID: 28765557 PMCID: PMC5539096 DOI: 10.1038/s41598-017-06700-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/16/2017] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium avium subsp. hominissuis is associated with infection of immunocompromised individuals as well as patients with chronic lung disease. M. avium infects macrophages and actively interfere with the host killing machinery such as apoptosis and autophagy. Bacteria alter the normal endosomal trafficking, prevent the maturation of phagosomes and modify many signaling pathways inside of the macrophage by secreting effector molecules into the cytoplasm. To investigate whether M. avium needs to attach to the internal surface of the vacuole membrane before releasing efferent molecules, vacuole membrane proteins were purified and binding to the surface molecules present in intracellular bacteria was evaluated. The voltage-dependent anion channels (VDAC) were identified as components of M. avium vacuoles in macrophages. M. avium mmpL4 proteins were found to bind to VDAC-1 protein. The inactivation of VDAC-1 function either by pharmacological means or siRNA lead to significant decrease of M. avium survival. Although, we could not establish a role of VDAC channels in the transport of known secreted M. avium proteins, we demonstrated that the porin channels are associated with the export of bacterial cell wall lipids outside of vacuole. Suppression of the host phagosomal transport systems and the pathogen transporter may serve as therapeutic targets for infectious diseases.
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Affiliation(s)
- Lia Danelishvili
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, OR, USA.
| | - Jessica J J Chinison
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, OR, USA.,Department of Microbiology, College of Science, Corvallis, OR, USA
| | - Tuan Pham
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Rashmi Gupta
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, OR, USA.,College of Medicine, University of Central Florida, Orlando, Florida, 32827, USA
| | - Luiz E Bermudez
- Department of Biomedical Sciences, College of Veterinary Medicine, Corvallis, OR, USA. .,Department of Microbiology, College of Science, Corvallis, OR, USA.
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18
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Nunes-Hasler P, Demaurex N. The ER phagosome connection in the era of membrane contact sites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1513-1524. [PMID: 28432021 DOI: 10.1016/j.bbamcr.2017.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 12/19/2022]
Abstract
Phagocytosis is an essential mechanism through which innate immune cells ingest foreign material that is either destroyed or used to generate and present antigens and initiate adaptive immune responses. While a role for the ER during phagosome biogenesis has been recognized, whether fusion with ER cisternae or vesicular derivatives occurs has been the source of much contention. Membrane contact sites (MCS) are tight appositions between ER membranes and various organelles that coordinate multiple functions including localized signalling, lipid transfer and trafficking. The discovery that MCS form between the ER and phagosomes now begs the question of whether MCS play a role in connecting the ER to phagosomes under different contexts. In this review, we consider the implications of MCS between the ER and phagosomes during cross-presentation and infection with intracellular pathogens. We also discuss the similarities between these contacts and those between the ER and plasma membrane and acidic organelles such as endosomes and lysosomes. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.
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Affiliation(s)
- Paula Nunes-Hasler
- Department of Cell Physiology and Metabolism, University of Geneva, Switzerland.
| | - Nicolas Demaurex
- Department of Cell Physiology and Metabolism, University of Geneva, Switzerland
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19
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Pauwels AM, Trost M, Beyaert R, Hoffmann E. Patterns, Receptors, and Signals: Regulation of Phagosome Maturation. Trends Immunol 2017; 38:407-422. [PMID: 28416446 PMCID: PMC5455985 DOI: 10.1016/j.it.2017.03.006] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/18/2017] [Accepted: 03/21/2017] [Indexed: 12/13/2022]
Abstract
Recognition of microbial pathogens and dead cells and their phagocytic uptake by specialized immune cells are essential to maintain host homeostasis. Phagosomes undergo fusion and fission events with endosomal and lysosomal compartments, a process called ‘phagosome maturation’, which leads to the degradation of the phagosomal content. However, many phagocytic cells also act as antigen-presenting cells and must balance degradation and peptide preservation. Emerging evidence indicates that receptor engagement by phagosomal cargo, as well as inflammatory mediators and cellular activation affect many aspects of phagosome maturation. Unsurprisingly, pathogens have developed strategies to hijack this machinery, thereby interfering with host immunity. Here, we highlight progress in this field, summarize findings on the impact of immune signals, and discuss consequences for pathogen elimination. Self and non-self immune signals are able to delay or accelerate phagosome maturation, and their effects are dependent on the phagocytic cell type, duration of stimulation, and whether the stimulus is particle bound or present in the cellular environment. Acceleration of phagosome maturation enhances pathogen killing, while a delay in phagosome maturation preserves antigenic peptides for presentation to T cells and to initiate adaptive immune responses. Besides its functions in pathogen killing and antigen presentation, the phagosome also functions as a signaling platform and interacts with other cell organelles. Some pathogens are able to arrest phagosome maturation to enhance their intraphagosomal survival and replication or to promote phagosomal escape. The latex bead phagocytosis model system combined with mass spectrometry is a powerful technique to analyze changes in the phagosomal proteome.
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Affiliation(s)
- Anne-Marie Pauwels
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Matthias Trost
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eik Hoffmann
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Current address: Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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20
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Dingjan I, Linders PTA, van den Bekerom L, Baranov MV, Halder P, Ter Beest M, van den Bogaart G. Oxidized phagosomal NOX2 complex is replenished from lysosomes. J Cell Sci 2017; 130:1285-1298. [PMID: 28202687 PMCID: PMC5399780 DOI: 10.1242/jcs.196931] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/09/2017] [Indexed: 12/11/2022] Open
Abstract
In dendritic cells, the NADPH oxidase 2 complex (NOX2) is recruited to the phagosomal membrane during antigen uptake. NOX2 produces reactive oxygen species (ROS) in the lumen of the phagosome that kill ingested pathogens, delay antigen breakdown and alter the peptide repertoire for presentation to T cells. How the integral membrane component of NOX2, cytochrome b558 (which comprises CYBB and CYBA), traffics to phagosomes is incompletely understood. In this study, we show in dendritic cells derived from human blood-isolated monocytes that cytochrome b558 is initially recruited to the phagosome from the plasma membrane during phagosome formation. Cytochrome b558 also traffics from a lysosomal pool to phagosomes and this is required to replenish oxidatively damaged NOX2. We identified syntaxin-7, SNAP23 and VAMP8 as the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins mediating this process. Our data describe a key mechanism of how dendritic cells sustain ROS production after antigen uptake that is required to initiate T cell responses. Highlighted Article: In human dendritic cells, the membrane component of the NADPH oxidase NOX2 complex is initially recruited to phagosomes from the plasma membrane, and oxidized NOX2 complex subunits are replenished from a lysosomal pool.
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Affiliation(s)
- Ilse Dingjan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Peter T A Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Luuk van den Bekerom
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Maksim V Baranov
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Partho Halder
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
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21
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Abstract
Phagocytosis and phagosome maturation are central to the development of the innate and adaptive immune response. Phagosome maturation is a continuous and dynamic process that occurs rapidly. In this chapter, we describe fluorescence-based live cell imaging methods for the quantitative and temporal analysis of phagosome maturation of latex beads and M. tuberculosis as two phagocytic targets. We also describe two simple protocols for monitoring phagosome maturation: the use of the acidotropic probe LysoTracker and analyzing the recruitment of EGFP-tagged host proteins by phagosomes.
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22
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Santos JC, Enninga J. At the crossroads: communication of bacteria-containing vacuoles with host organelles. Cell Microbiol 2016; 18:330-9. [PMID: 26762760 DOI: 10.1111/cmi.12567] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 02/06/2023]
Abstract
Invasive bacterial pathogens are engulfed upon host cell entry in a vacuolar environment called the bacteria-containing vacuole (BCV). BCVs directly contact with numerous host compartments, mainly vesicles of the endocytic pathway, such as endosomes or lysosomes. In addition, they also interact with the endoplasmic reticulum and endomembranes of the secretory pathway. These connections between the pathogen and the host occur either through heterotypic membrane fusions or through membrane contact sites. The precise regulation of BCV contacts with host compartments defines the constitution of the intracellular bacterial niche. It emerges that the associated pathways may control the stability of the BCV resulting either in vacuolar or cytoplasmically growing bacteria. Here, we will portray how the usage of novel proteomics and imaging technologies allows comparison of the communication of different host cell compartments with four relevant intracellular human pathogens, namely Salmonella enterica, Legionella pneumophila, Shigella flexneri and Francisella tularensis. The first two remain mainly within the BCV, and the latter two escape into the cytoplasm.
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Affiliation(s)
- José Carlos Santos
- Unit "Dynamics of Host-Pathogen Interactions", Institut Pasteur, Paris, France
| | - Jost Enninga
- Unit "Dynamics of Host-Pathogen Interactions", Institut Pasteur, Paris, France
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23
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Hanadate Y, Saito-Nakano Y, Nakada-Tsukui K, Nozaki T. Endoplasmic reticulum-resident Rab8A GTPase is involved in phagocytosis in the protozoan parasite Entamoeba histolytica. Cell Microbiol 2016; 18:1358-73. [PMID: 26807810 PMCID: PMC5071775 DOI: 10.1111/cmi.12570] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 12/31/2015] [Accepted: 01/19/2016] [Indexed: 12/20/2022]
Abstract
Phagocytosis is indispensable for the pathogenesis of the intestinal protozoan parasite Entamoeba histolytica. Here, we showed that in E. histolytica Rab8A, which is generally involved in trafficking from the trans‐Golgi network to the plasma membrane in other organisms but was previously identified in phagosomes of the amoeba in the proteomic analysis, primarily resides in the endoplasmic reticulum (ER) and participates in phagocytosis. We demonstrated that down‐regulation of EhRab8A by small antisense RNA‐mediated transcriptional gene silencing remarkably reduced adherence and phagocytosis of erythrocytes, bacteria and carboxylated latex beads. Surface biotinylation followed by SDS‐PAGE analysis revealed that the surface expression of several proteins presumably involved in target recognition was reduced in the EhRab8A gene‐silenced strain. Further, overexpression of wild‐type EhRab8A augmented phagocytosis, whereas expression of the dominant‐negative form of EhRab8A resulted in reduced phagocytosis. These results indicated that EhRab8A regulates transport of surface receptor(s) for the prey from the ER to the plasma membrane. To our knowledge, this is the first report that the ER‐resident Rab GTPase is involved in phagocytosis through the regulation of trafficking of a surface receptor, supporting a premise of direct involvement of the ER in phagocytosis.
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Affiliation(s)
- Yuki Hanadate
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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24
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Freitag M. The kinetochore interaction network (KIN) of ascomycetes. Mycologia 2016; 108:485-505. [PMID: 26908646 DOI: 10.3852/15-182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 01/13/2023]
Abstract
Chromosome segregation relies on coordinated activity of a large assembly of proteins, the kinetochore interaction network (KIN). How conserved the underlying mechanisms driving the epigenetic phenomenon of centromere and kinetochore assembly and maintenance are remains unclear, even though various eukaryotic models have been studied. More than 50 different proteins, many in multiple copies, comprise the KIN or are associated with fungal centromeres and kinetochores. Proteins isolated from immune sera recognized centromeric regions on chromosomes and thus were named centromere proteins (CENPs). CENP-A, sometimes called centromere-specific H3 (CenH3), is incorporated into nucleosomes within or near centromeres. The constitutive centromere-associated network (CCAN) assembles on this specialized chromatin, likely based on specific interactions with and requiring presence of CENP-C. The outer kinetochore comprises the Knl1-Mis12-Ndc80 (KMN) protein complexes that connect CCAN to spindles, accomplished by binding and stabilizing microtubules (MTs) and in the process generating load-bearing assemblies for chromatid segregation. In most fungi the Dam1/DASH complex connects the KMN complexes to MTs. Fungi present a rich resource to investigate mechanistic commonalities but also differences in kinetochore architecture. While ascomycetes have sets of CCAN and KMN proteins that are conserved with those of budding yeast or metazoans, searching other major branches of the fungal kingdom revealed that CCAN proteins are poorly conserved at the primary sequence level. Several conserved binding motifs or domains within KMN complexes have been described recently, and these features of ascomycete KIN proteins are shared with most metazoan proteins. In addition, several ascomycete-specific domains have been identified here.
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305
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25
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de Araújo MEG, Lamberti G, Huber LA. Purification of Early and Late Endosomes. Cold Spring Harb Protoc 2015; 2015:pdb.top074443. [PMID: 26631131 DOI: 10.1101/pdb.top074443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proteomic analysis of early and late endosomes has been constrained by the limited purity of the endosomal fractions that can be achieved by biochemical methods. Here we briefly review endocytic pathways, and then introduce fractionation strategies that have been used to improve the purity of isolated endosomes. In addition, we describe innovative proteomics analysis methods that have been shown to partially circumvent the limitations found in the enrichment steps.
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Affiliation(s)
- Mariana E G de Araújo
- Biocenter, Division of Cell Biology, Innsbruck Medical University, A-6020 Innsbruck, Austria
| | - Giorgia Lamberti
- Biocenter, Division of Cell Biology, Innsbruck Medical University, A-6020 Innsbruck, Austria
| | - Lukas A Huber
- Biocenter, Division of Cell Biology, Innsbruck Medical University, A-6020 Innsbruck, Austria
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26
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Molecular imaging analysis of Rab GTPases in the regulation of phagocytosis and macropinocytosis. Anat Sci Int 2015; 91:35-42. [DOI: 10.1007/s12565-015-0313-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/26/2015] [Indexed: 12/22/2022]
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27
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Naj X, Linder S. ER-Coordinated Activities of Rab22a and Rab5a Drive Phagosomal Compaction and Intracellular Processing of Borrelia burgdorferi by Macrophages. Cell Rep 2015; 12:1816-30. [DOI: 10.1016/j.celrep.2015.08.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 06/24/2015] [Accepted: 08/08/2015] [Indexed: 01/26/2023] Open
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Santos JC, Duchateau M, Fredlund J, Weiner A, Mallet A, Schmitt C, Matondo M, Hourdel V, Chamot-Rooke J, Enninga J. The COPII complex and lysosomal VAMP7 determine intracellular Salmonella localization and growth. Cell Microbiol 2015; 17:1699-720. [PMID: 26084942 DOI: 10.1111/cmi.12475] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/22/2015] [Accepted: 06/12/2015] [Indexed: 12/18/2022]
Abstract
Salmonella invades epithelial cells and survives within a membrane-bound compartment, the Salmonella-containing vacuole (SCV). We isolated and determined the host protein composition of the SCV at 30 min and 3 h of infection to identify and characterize novel regulators of intracellular bacterial localization and growth. Quantitation of the SCV protein content revealed 392 host proteins specifically enriched at SCVs, out of which 173 associated exclusively with early SCVs, 124 with maturing SCV and 95 proteins during both time-points. Vacuole interactions with endoplasmic reticulum-derived coat protein complex II vesicles modulate early steps of SCV maturation, promoting SCV rupture and bacterial hyper-replication within the host cytosol. On the other hand, SCV interactions with VAMP7-positive lysosome-like vesicles promote Salmonella-induced filament formation and bacterial growth within the late SCV. Our results reveal that the dynamic communication between the SCV and distinct host organelles affects both intracellular Salmonella localization and growth at successive steps of host cell invasion.
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Affiliation(s)
- José Carlos Santos
- Unit of Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France.,Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, Portugal
| | - Magalie Duchateau
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, Paris, France
| | - Jennifer Fredlund
- Unit of Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France
| | - Allon Weiner
- Unit of Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France
| | - Adeline Mallet
- Plate-forme Microscopie Ultrastructurale, Institut Pasteur, Paris, France
| | - Christine Schmitt
- Plate-forme Microscopie Ultrastructurale, Institut Pasteur, Paris, France
| | - Mariette Matondo
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, Paris, France
| | - Véronique Hourdel
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, Paris, France
| | - Julia Chamot-Rooke
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, Paris, France.,CNRS UMR3528, Paris, France
| | - Jost Enninga
- Unit of Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France
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29
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Herweg JA, Hansmeier N, Otto A, Geffken AC, Subbarayal P, Prusty BK, Becher D, Hensel M, Schaible UE, Rudel T, Hilbi H. Purification and proteomics of pathogen-modified vacuoles and membranes. Front Cell Infect Microbiol 2015; 5:48. [PMID: 26082896 PMCID: PMC4451638 DOI: 10.3389/fcimb.2015.00048] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/14/2015] [Indexed: 01/08/2023] Open
Abstract
Certain pathogenic bacteria adopt an intracellular lifestyle and proliferate in eukaryotic host cells. The intracellular niche protects the bacteria from cellular and humoral components of the mammalian immune system, and at the same time, allows the bacteria to gain access to otherwise restricted nutrient sources. Yet, intracellular protection and access to nutrients comes with a price, i.e., the bacteria need to overcome cell-autonomous defense mechanisms, such as the bactericidal endocytic pathway. While a few bacteria rupture the early phagosome and escape into the host cytoplasm, most intracellular pathogens form a distinct, degradation-resistant and replication-permissive membranous compartment. Intracellular bacteria that form unique pathogen vacuoles include Legionella, Mycobacterium, Chlamydia, Simkania, and Salmonella species. In order to understand the formation of these pathogen niches on a global scale and in a comprehensive and quantitative manner, an inventory of compartment-associated host factors is required. To this end, the intact pathogen compartments need to be isolated, purified and biochemically characterized. Here, we review recent progress on the isolation and purification of pathogen-modified vacuoles and membranes, as well as their proteomic characterization by mass spectrometry and different validation approaches. These studies provide the basis for further investigations on the specific mechanisms of pathogen-driven compartment formation.
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Affiliation(s)
- Jo-Ana Herweg
- Chair of Microbiology, Biocenter, University of Würzburg Würzburg, Germany
| | - Nicole Hansmeier
- Division of Microbiology, University of Osnabrück Osnabrück, Germany
| | - Andreas Otto
- Institute of Microbiology, Ernst-Moritz-Arndt University Greifswald Greifswald, Germany
| | - Anna C Geffken
- Priority Area Infections, Cellular Microbiology, Research Center Borstel, Leibniz Center for Medicine and Biosciences Borstel, Germany
| | - Prema Subbarayal
- Chair of Microbiology, Biocenter, University of Würzburg Würzburg, Germany
| | - Bhupesh K Prusty
- Chair of Microbiology, Biocenter, University of Würzburg Würzburg, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt University Greifswald Greifswald, Germany
| | - Michael Hensel
- Division of Microbiology, University of Osnabrück Osnabrück, Germany
| | - Ulrich E Schaible
- Priority Area Infections, Cellular Microbiology, Research Center Borstel, Leibniz Center for Medicine and Biosciences Borstel, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg Würzburg, Germany
| | - Hubert Hilbi
- Department of Medicine, Max von Pettenkofer Institute, Ludwig-Maximilians University Munich Munich, Germany ; Department of Medicine, Institute of Medical Microbiology, University of Zürich Zürich, Switzerland
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Rab14 regulates maturation of macrophage phagosomes containing the fungal pathogen Candida albicans and outcome of the host-pathogen interaction. Infect Immun 2015; 83:1523-35. [PMID: 25644001 PMCID: PMC4363425 DOI: 10.1128/iai.02917-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avoidance of innate immune defense is an important mechanism contributing to the pathogenicity of microorganisms. The fungal pathogen Candida albicans undergoes morphogenetic switching from the yeast to the filamentous hyphal form following phagocytosis by macrophages, facilitating its escape from the phagosome, which can result in host cell lysis. We show that the intracellular host trafficking GTPase Rab14 plays an important role in protecting macrophages from lysis mediated by C. albicans hyphae. Live-cell imaging of macrophages expressing green fluorescent protein (GFP)-tagged Rab14 or dominant negative Rab14, or with small interfering RNA (siRNA)-mediated knockdown of Rab14, revealed the temporal dynamics of this protein and its influence on the maturation of macrophage phagosomes following the engulfment of C. albicans cells. Phagosomes containing live C. albicans cells became transiently Rab14 positive within 2 min following engulfment. The duration of Rab14 retention on phagosomes was prolonged for hyphal cargo and was directly proportional to hyphal length. Interference with endogenous Rab14 did not affect the migration of macrophages toward C. albicans cells, the rate of engulfment, the overall uptake of fungal cells, or early phagosome processing. However, Rab14 depletion delayed the acquisition of the late phagosome maturation markers LAMP1 and lysosomal cathepsin, indicating delayed formation of a fully bioactive lysosome. This was associated with a significant increase in the level of macrophage killing by C. albicans. Therefore, Rab14 activity promotes phagosome maturation during C. albicans infection but is dysregulated on the phagosome in the presence of the invasive hyphal form, which favors fungal survival and escape.
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31
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Omosigho NN, Swaminathan K, Plomann M, Müller-Taubenberger A, Noegel AA, Riyahi TY. The Dictyostelium discoideum RACK1 orthologue has roles in growth and development. Cell Commun Signal 2014; 12:37. [PMID: 24930026 PMCID: PMC4094278 DOI: 10.1186/1478-811x-12-37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/06/2014] [Indexed: 12/19/2022] Open
Abstract
Background The receptor for activated C-kinase 1 (RACK1) is a conserved protein belonging to the WD40 repeat family of proteins. It folds into a beta propeller with seven blades which allow interactions with many proteins. Thus it can serve as a scaffolding protein and have roles in several cellular processes. Results We identified the product of the Dictyostelium discoideum gpbB gene as the Dictyostelium RACK1 homolog. The protein is mainly cytosolic but can also associate with cellular membranes. DdRACK1 binds to phosphoinositides (PIPs) in protein-lipid overlay and liposome-binding assays. The basis of this activity resides in a basic region located in the extended loop between blades 6 and 7 as revealed by mutational analysis. Similar to RACK1 proteins from other organisms DdRACK1 interacts with G protein subunits alpha, beta and gamma as shown by yeast two-hybrid, pulldown, and immunoprecipitation assays. Unlike the Saccharomyces cerevisiae and Cryptococcus neoformans RACK1 proteins it does not appear to take over Gβ function in D. discoideum as developmental and other defects were not rescued in Gβ null mutants overexpressing GFP-DdRACK1. Overexpression of GFP-tagged DdRACK1 and a mutant version (DdRACK1mut) which carried a charge-reversal mutation in the basic region in wild type cells led to changes during growth and development. Conclusion DdRACK1 interacts with heterotrimeric G proteins and can through these interactions impact on processes specifically regulated by these proteins.
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Affiliation(s)
| | | | | | | | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Köln, Germany.
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32
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Bronietzki M, Kasmapour B, Gutierrez MG. Study of phagolysosome biogenesis in live macrophages. J Vis Exp 2014. [PMID: 24638150 DOI: 10.3791/51201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phagocytic cells play a major role in the innate immune system by removing and eliminating invading microorganisms in their phagosomes. Phagosome maturation is the complex and tightly regulated process during which a nascent phagosome undergoes drastic transformation through well-orchestrated interactions with various cellular organelles and compartments in the cytoplasm. This process, which is essential for the physiological function of phagocytic cells by endowing phagosomes with their lytic and bactericidal properties, culminates in fusion of phagosomes with lysosomes and biogenesis of phagolysosomes which is considered to be the last and critical stage of maturation for phagosomes. In this report, we describe a live cell imaging based method for qualitative and quantitative analysis of the dynamic process of lysosome to phagosome content delivery, which is a hallmark of phagolysosome biogenesis. This approach uses IgG-coated microbeads as a model for phagocytosis and fluorophore-conjugated dextran molecules as a luminal lysosomal cargo probe, in order to follow the dynamic delivery of lysosomal content to the phagosomes in real time in live macrophages using time-lapse imaging and confocal laser scanning microscopy. Here we describe in detail the background, the preparation steps and the step-by-step experimental setup to enable easy and precise deployment of this method in other labs. Our described method is simple, robust, and most importantly, can be easily adapted to study phagosomal interactions and maturation in different systems and under various experimental settings such as use of various phagocytic cells types, loss-of-function experiments, different probes, and phagocytic particles.
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Affiliation(s)
- Marc Bronietzki
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research
| | - Bahram Kasmapour
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research
| | - Maximiliano Gabriel Gutierrez
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research; Division of Mycobacterial Research, National Institute for Medical Research;
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33
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Protein synthesis rate is the predominant regulator of protein expression during differentiation. Mol Syst Biol 2014; 9:689. [PMID: 24045637 PMCID: PMC3792347 DOI: 10.1038/msb.2013.47] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/21/2013] [Indexed: 12/12/2022] Open
Abstract
The contribution of transcription, protein synthesis and degradation rates to the control of protein expression during differentiation was analyzed using quantitative proteomics and transcriptomics data. Protein synthesis rate was identified as the main determinant of protein expression. ![]()
The lack of correlation usually observed between transcript and protein levels can be fully explained when correcting for the synthesis and degradation rates of the individual proteins. Synthesis rates for individual proteins are extensively regulated, in contrast to degradation rates that mostly remain constant in response to differentiation. The modularity of macromolecular complexes is maintained during synthesis and degradation of the complexes.
External perturbations, by forcing cells to adapt to a new environment, often elicit large-scale changes in gene expression resulting in an altered proteome that improves the cell's fitness in the new conditions. Steady-state levels of a proteome depend on transcription, the levels of transcripts, translation and protein degradation but system-level contribution that each of these processes make to the final protein expression change has yet to be explored. We therefore applied a systems biology approach to characterize the regulation of protein expression during cellular differentiation using quantitative proteomics. As a general rule, it seems that protein expression during cellular differentiation is largely controlled by changes in the relative synthesis rate, whereas the relative degradation rate of the majority of proteins stays constant. In these data, we also observe that the proteins in defined sub-structures of larger protein complexes tend to have highly correlated synthesis and degradation rates but that this does not necessarily extend to the holo-complex. Finally, we provide strong evidence that the generally poor correlation observed between transcript and protein levels can fully be explained once the protein synthesis and degradation rates are taken into account.
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34
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Pan X, Whitten DA, Wilkerson CG, Pestka JJ. Dynamic changes in ribosome-associated proteome and phosphoproteome during deoxynivalenol-induced translation inhibition and ribotoxic stress. Toxicol Sci 2013; 138:217-33. [PMID: 24284785 DOI: 10.1093/toxsci/kft270] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Deoxynivalenol (DON), a trichothecene mycotoxin produced by Fusarium that commonly contaminates cereal-based food, interacts with the ribosome to cause translation inhibition and activate stress kinases in mononuclear phagocytes via the ribotoxic stress response (RSR). The goal of this study was to test the hypothesis that the ribosome functions as a platform for spatiotemporal regulation of translation inhibition and RSR. Specifically, we employed stable isotope labeling of amino acids in cell culture (SILAC)-based proteomics to quantify the early (≤ 30 min) DON-induced changes in ribosome-associated proteins in RAW 264.7 murine macrophage. Changes in the proteome and phosphoproteome were determined using off-gel isoelectric focusing and titanium dioxide chromatography, respectively, in conjunction with LC-MS/MS. Following exposure of RAW 264.7 to a toxicologically relevant concentration of DON (250 ng/ml), we observed an overall decrease in translation-related proteins interacting with the ribosome, concurrently with a compensatory increase in proteins that mediate protein folding, biosynthesis, and cellular organization. Alterations in the ribosome-associated phosphoproteome reflected proteins that modulate translational and transcriptional regulation, and others that converged with signaling pathways known to overlap with phosphorylation changes characterized previously in intact RAW 264.7 cells. These results suggest that the ribosome plays a central role as a hub for association and phosphorylation of proteins involved in the coordination of early translation inhibition as well as recruitment and maintenance of stress-related proteins-both of which enable cells to adapt and respond to ribotoxin exposure. This study provides a template for elucidating the molecular mechanisms of DON and other ribosome-targeting agents.
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Affiliation(s)
- Xiao Pan
- * Department of Biochemistry and Molecular Biology
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35
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Garg A, Wu LP. Drosophila Rab14 mediates phagocytosis in the immune response to Staphylococcus aureus. Cell Microbiol 2013; 16:296-310. [PMID: 24119134 DOI: 10.1111/cmi.12220] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 01/20/2023]
Abstract
Drosophila haemocytes are essential for the animal to resist Staphylococcus aureus infections. Phagocytosis is a central component of the haemocyte-mediated immune response. It involves regulated interaction between the phagocytic and the endocytic compartments. RabGTPases are pivotal for the membrane trafficking and fusion events, and thus are often targets of intracellular pathogens that subvert phagocytosis. An in vivo screen identified Rab2 and Rab14 as candidates for proteins regulating phagosome maturation. Since Rab14 is often targeted by intracellular pathogens, an understanding of its function during phagocytosis and the overall immune response can give insight into the pathogenesis of intracellular microbes. We generated a Drosophila Rab14 mutant and characterized the resulting immune defects in animals and specifically in haemocytes in response to an S. aureus infection. Haemocyte based immunofluorescence studies indicate that Rab14 is recruited to the phagosome and like Rab7, a well-characterized regulator of the phagocytic pathway, is essential for progression of phagosome maturation. Rab14 mutant haemocytes show impaired recruitment of Rab7 and of a lysosomal marker onto S. aureus phagosomes. The defect in phagocytosis is associated with higher bacterial load and increased susceptibility to S. aureus in the animal.
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Affiliation(s)
- Aprajita Garg
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
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36
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Kastl L, Sasse D, Wulf V, Hartmann R, Mircheski J, Ranke C, Carregal-Romero S, Martínez-López JA, Fernández-Chacón R, Parak WJ, Elsasser HP, Rivera Gil P. Multiple internalization pathways of polyelectrolyte multilayer capsules into mammalian cells. ACS NANO 2013; 7:6605-6618. [PMID: 23826767 DOI: 10.1021/nn306032k] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Polyelectrolyte multilayer (PEM) capsules are carrier vehicles with great potential for biomedical applications. With the future aim of designing biocompatible, effective therapeutic delivery systems (e.g., for cancer), the pathway of internalization (uptake and fate) of PEM capsules was investigated. In particular the following experiments were performed: (i) the study of capsule co-localization with established endocytic markers, (ii) switching-off endocytotic pathways with pharmaceutical/chemical inhibitors, and (iii) characterization and quantification of capsule uptake with confocal and electron microscopy. As result, capsules co-localized with lipid rafts and with phagolysosomes, but not with other endocytic vesicles. Chemical interference of endocytosis with chemical blockers indicated that PEM capsules enter the investigated cell lines through a mechanism slightly sensitive to electrostatic interactions, independent of clathrin and caveolae, and strongly dependent on cholesterol-rich domains and organelle acidification. Microscopic characterization of cells during capsule uptake showed the formation of phagocytic cups (vesicles) to engulf the capsules, an increased number of mitochondria, and a final localization in the perinuclear cytoplasma. Combining all these indicators we conclude that PEM capsule internalization in general occurs as a combination of different sequential mechanisms. Initially, an adsorptive mechanism due to strong electrostatic interactions governs the stabilization of the capsules at the cell surface. Membrane ruffling and filopodia extensions are responsible for capsule engulfing through the formation of a phagocytic cup. Co-localization with lipid raft domains activates the cell to initiate a lipid-raft-mediated macropinocytosis. Internalization vesicles are very acidic and co-localize only with phagolysosome markers, excluding caveolin-mediated pathways and indicating that upon phagocytosis the capsules are sorted to heterophagolysosomes.
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Affiliation(s)
- Lena Kastl
- Fachbereich Physik, Philipps-Universität Marburg, Renthof 7, 35037 Marburg, Germany
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Abstract
Rab GTPases are at the central node of the machinery that regulates trafficking of organelles, including phagosomes. Thanks to the unique combination of high quality phagosome purification with highly sensitive proteomic studies, the network of Rab proteins that are dynamically associated with phagosomes during the process of maturation of this organelle is relatively well known. Whereas the phagosomal functions of many of the Rab proteins associated with phagosomes are characterized, the role(s) of most of these trafficking regulators remains to be identified. In some cases, even when the function in the context of phagosome biology is described, phagosomal Rab proteins seem to have similar roles. This review summarizes the current knowledge about the identity and function of phagosomal Rab GTPases, with a particular emphasis on new evidence that clarify these seemingly overlapping Rab functions during phagosome maturation.
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Kasmapour B, Cai L, Gutierrez MG. Spatial distribution of phagolysosomes is independent of the regulation of lysosome position by Rab34. Int J Biochem Cell Biol 2013; 45:2057-65. [PMID: 23871933 DOI: 10.1016/j.biocel.2013.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 11/20/2022]
Abstract
Within a cell, the regulation of organelle positioning is considered to be critical in spatio-temporal responses. The position of late endocytic organelles (named here lysosomes for simplicity) is tightly controlled and has a functional impact on processes like endocytosis, phagocytosis and autophagocytosis. The cytoplasmic distribution profile of lysosomes can be easily determined in cells where the cytoplasm/nuclear ratio in a cross-section area is high. However, determining lysosomal position in cells with lower cytoplasm/nuclear ratio, such as macrophages is more challenging. Here, we describe a method that can be efficiently and accurately used to determine the position of organelles in macrophages using confocal microscopy in two-dimensional (2D) images. Using this approach in macrophages, we confirmed previous observations in epithelial cells that both changes in cytoplasmic pH and the levels of active Rab34 induced a re-distribution of lysosomes to the cell centre or periphery. Noteworthy is that this Rab34-dependent re-distribution of lysosomes did not significantly affect the spatial distribution profile of phagolysosomes in the cytoplasm. We conclude that although Rab34 regulates both lysosomal positioning and lysosome to phagosome fusion, the latter effect is not due to the regulation of the cytoplasmic accessibility of lysosomes to phagosomes by Rab34.
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Affiliation(s)
- Bahram Kasmapour
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A. An extended proteome map of the lysosomal membrane reveals novel potential transporters. Mol Cell Proteomics 2013; 12:1572-88. [PMID: 23436907 PMCID: PMC3675815 DOI: 10.1074/mcp.m112.021980] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Lysosomes are membrane-bound endocytic organelles that play a major role in degrading cell macromolecules and recycling their building blocks. A comprehensive knowledge of the lysosome function requires an extensive description of its content, an issue partially addressed by previous proteomic analyses. However, the proteins underlying many lysosomal membrane functions, including numerous membrane transporters, remain unidentified. We performed a comparative, semi-quantitative proteomic analysis of rat liver lysosome-enriched and lysosome-nonenriched membranes and used spectral counts to evaluate the relative abundance of proteins. Among a total of 2,385 identified proteins, 734 proteins were significantly enriched in the lysosomal fraction, including 207 proteins already known or predicted as endo-lysosomal and 94 proteins without any known or predicted subcellular localization. The remaining 433 proteins had been previously assigned to other subcellular compartments but may in fact reside on lysosomes either predominantly or as a secondary location. Many membrane-associated complexes implicated in diverse processes such as degradation, membrane trafficking, lysosome biogenesis, lysosome acidification, signaling, and nutrient sensing were enriched in the lysosomal fraction. They were identified to an unprecedented extent as most, if not all, of their subunits were found and retained by our screen. Numerous transporters were also identified, including 46 novel potentially lysosomal proteins. We expressed 12 candidates in HeLa cells and observed that most of them colocalized with the lysosomal marker LAMP1, thus confirming their lysosomal residency. This list of candidate lysosomal proteins substantially increases our knowledge of the lysosomal membrane and provides a basis for further characterization of lysosomal functions.
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Affiliation(s)
- Agnès Chapel
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Sylvie Kieffer-Jaquinod
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Corinne Sagné
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Quentin Verdon
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
- §§Graduate School ED 419, Université Paris-Sud 11, Hôpital Bicêtre, F-94276 Le Kremlin Bicêtre France, and
| | - Corinne Ivaldi
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Mourad Mellal
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jaqueline Thirion
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Michel Jadot
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Christophe Bruley
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jérôme Garin
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Bruno Gasnier
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Agnès Journet
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
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40
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Wavre-Shapton ST, Tolmachova T, da Silva ML, Futter CE, Seabra MC. Conditional ablation of the choroideremia gene causes age-related changes in mouse retinal pigment epithelium. PLoS One 2013; 8:e57769. [PMID: 23460904 PMCID: PMC3584022 DOI: 10.1371/journal.pone.0057769] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 01/25/2013] [Indexed: 01/25/2023] Open
Abstract
The retinal pigment epithelium (RPE) is a pigmented monolayer of cells lying between the photoreceptors and a layer of fenestrated capillaries, the choriocapillaris. Choroideremia (CHM) is an X-linked progressive degeneration of these three layers caused by the loss of function of Rab Escort protein-1 (REP1). REP1 is involved in the prenylation of Rab proteins, key regulators of membrane trafficking. To study the pathological consequences of chronic disruption of membrane traffic in the RPE we used a cell type-specific knock-out mouse model of the disease, where the Chm/Rep1 gene is deleted only in pigmented cells (ChmFlox, Tyr-Cre+). Transmission electron microscopy (TEM) was used to quantitate the melanosome distribution in the RPE and immunofluorescent staining of rhodopsin was used to quantitate phagocytosed rod outer segments in retinal sections. The ultrastructure of the RPE and Bruch’s membrane at different ages was characterised by TEM to analyse age-related changes occurring as a result of defects in membrane traffic pathways. Chm/Rep1 gene knockout in RPE cells resulted in reduced numbers of melanosomes in the apical processes and delayed phagosome degradation. In addition, the RPE accumulated pathological changes at 5–6 months of age similar to those observed in 2-year old controls. These included the intracellular accumulation of lipofuscin-containing deposits, disorganised basal infoldings and the extracellular accumulation of basal laminar and basal linear deposits. The phenotype of the ChmFlox, Tyr-Cre+ mice suggests that loss of the Chm/Rep1 gene causes premature accumulation of features of aging in the RPE. Furthermore, the striking similarities between the present observations and some of the phenotypes reported in age-related macular degeneration (AMD) suggest that membrane traffic defects may contribute to the pathogenesis of AMD.
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Affiliation(s)
- Silène T. Wavre-Shapton
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Tanya Tolmachova
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Mafalda Lopes da Silva
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Clare E. Futter
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
- * E-mail: (CEF); (MCS)
| | - Miguel C. Seabra
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (CEF); (MCS)
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41
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Pan X, Whitten DA, Wu M, Chan C, Wilkerson CG, Pestka JJ. Global protein phosphorylation dynamics during deoxynivalenol-induced ribotoxic stress response in the macrophage. Toxicol Appl Pharmacol 2013; 268:201-11. [PMID: 23352502 DOI: 10.1016/j.taap.2013.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/12/2013] [Accepted: 01/14/2013] [Indexed: 11/27/2022]
Abstract
Deoxynivalenol (DON), a trichothecene mycotoxin produced by Fusarium that commonly contaminates food, is capable of activating mononuclear phagocytes of the innate immune system via a process termed the ribotoxic stress response (RSR). To encapture global signaling events mediating RSR, we quantified the early temporal (≤30min) phosphoproteome changes that occurred in RAW 264.7 murine macrophage during exposure to a toxicologically relevant concentration of DON (250ng/mL). Large-scale phosphoproteomic analysis employing stable isotope labeling of amino acids in cell culture (SILAC) in conjunction with titanium dioxide chromatography revealed that DON significantly upregulated or downregulated phosphorylation of 188 proteins at both known and yet-to-be functionally characterized phosphosites. DON-induced RSR is extremely complex and goes far beyond its prior known capacity to inhibit translation and activate MAPKs. Transcriptional regulation was the main target during early DON-induced RSR, covering over 20% of the altered phosphoproteins as indicated by Gene Ontology annotation and including transcription factors/cofactors and epigenetic modulators. Other biological processes impacted included cell cycle, RNA processing, translation, ribosome biogenesis, monocyte differentiation and cytoskeleton organization. Some of these processes could be mediated by signaling networks involving MAPK-, NFκB-, AKT- and AMPK-linked pathways. Fuzzy c-means clustering revealed that DON-regulated phosphosites could be discretely classified with regard to the kinetics of phosphorylation/dephosphorylation. The cellular response networks identified provide a template for further exploration of the mechanisms of trichothecenemycotoxins and other ribotoxins, and ultimately, could contribute to improved mechanism-based human health risk assessment.
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Affiliation(s)
- Xiao Pan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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42
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Size-dependent mechanism of cargo sorting during lysosome-phagosome fusion is controlled by Rab34. Proc Natl Acad Sci U S A 2012. [PMID: 23197834 DOI: 10.1073/pnas.1206811109] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Phagosome maturation is an essential part of the innate and adaptive immune response. Although it is well established that several Ras-related proteins in brain (Rab) proteins become associated to phagosomes, little is known about how these phagosomal Rab proteins influence phagosome maturation. Here, we show a specific role for Rab34 and mammalian uncoordinated 13-2 (Munc13-2) in phagolysosome biogenesis and cargo delivery. Rab34 knockdown impaired the fusion of phagosomes with late endosomes/lysosomes and high levels of active Rab34 promoted this process. We demonstrate that Rab34 enhances phagosome maturation independently of Rab7 and coordinates phagolysosome biogenesis through size-selective transfer of late endosomal/lysosomal cargo into phagosomes. More importantly, we show that Rab34 mediates phagosome maturation through the recruitment of the protein Munc13-2. Finally, we report that the alternative maturation pathway controlled by Rab34 is critical for mycobacterial killing because Rab34 silencing resulted in mycobacterial survival, and Rab34 expression led to mycobacterial killing. Altogether, our studies uncover Rab34/Munc13-2 as a critical part of an alternative Rab7-independent phagosome maturation machinery and lysosome-mediated killing of mycobacteria.
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43
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Stein MP, Müller MP, Wandinger-Ness A. Bacterial pathogens commandeer Rab GTPases to establish intracellular niches. Traffic 2012; 13:1565-88. [PMID: 22901006 DOI: 10.1111/tra.12000] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 08/13/2012] [Indexed: 12/11/2022]
Abstract
Intracellular bacterial pathogens deploy virulence factors termed effectors to inhibit degradation by host cells and to establish intracellular niches where growth and differentiation take place. Here, we describe mechanisms by which human bacterial pathogens (including Chlamydiae; Coxiella burnetii; Helicobacter pylori; Legionella pneumophila; Listeria monocytogenes; Mycobacteria; Pseudomonas aeruginosa, Salmonella enterica) modulate endocytic and exocytic Rab GTPases in order to thrive in host cells. Host cell Rab GTPases are critical for intracellular transport following pathogen phagocytosis or endocytosis. At the molecular level bacterial effectors hijack Rab protein function to: evade degradation, direct transport to particular intracellular locations and monopolize host vesicles carrying molecules that are needed for a stable niche and/or bacterial growth and differentiation. Bacterial effectors may serve as specific receptors for Rab GTPases or as enzymes that post-translationally modify Rab proteins or endosomal membrane lipids required for Rab function. Emerging data indicate that bacterial effector expression is temporally and spatially regulated and multiple virulence factors may act concertedly to usurp Rab GTPase function, alter signaling and ensure niche establishment and intracellular bacterial growth, making this field an exciting area for further study.
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Affiliation(s)
- Mary-Pat Stein
- Department of Biology, California State University, Northridge, Northridge, CA, USA.
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44
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Paschke P, Pawolleck N, Haenel F, Otto H, Rühling H, Maniak M. The isoform B of the Dictyostelium long-chain fatty-acyl-coenzyme A synthetase is initially inserted into the ER and subsequently provides peroxisomes with an activity important for efficient phagocytosis. Eur J Cell Biol 2012; 91:717-27. [DOI: 10.1016/j.ejcb.2012.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 03/27/2012] [Accepted: 03/29/2012] [Indexed: 11/27/2022] Open
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45
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Kristensen AR, Gsponer J, Foster LJ. A high-throughput approach for measuring temporal changes in the interactome. Nat Methods 2012; 9:907-9. [PMID: 22863883 PMCID: PMC3954081 DOI: 10.1038/nmeth.2131] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/27/2012] [Indexed: 01/01/2023]
Abstract
Interactomes are often measured using affinity purification-mass spectrometry (AP-MS) or yeast two-hybrid approaches, but these methods do not provide stoichiometric or temporal information. We combine quantitative proteomics and size-exclusion chromatography to map 291 coeluting complexes. This method allows mapping of an interactome to the same depth and accuracy as AP-MS with less work and without overexpression or tagging. The use of triplex labeling enables monitoring of interactome rearrangements.
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Affiliation(s)
- Anders R Kristensen
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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46
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Goyette G, Boulais J, Carruthers NJ, Landry CR, Jutras I, Duclos S, Dermine JF, Michnick SW, LaBoissière S, Lajoie G, Barreiro L, Thibault P, Desjardins M. Proteomic characterization of phagosomal membrane microdomains during phagolysosome biogenesis and evolution. Mol Cell Proteomics 2012; 11:1365-77. [PMID: 22915823 DOI: 10.1074/mcp.m112.021048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After their formation at the cell surface, phagosomes become fully functional through a complex maturation process involving sequential interactions with various intracellular organelles. In the last decade, series of data indicated that some of the phagosome functional properties occur in specialized membrane microdomains. The molecules associated with membrane microdomains, as well as the organization of these structures during phagolysosome biogenesis are largely unknown. In this study, we combined proteomics and bioinformatics analyses to characterize the dynamic association of proteins to maturing phagosomes. Our data indicate that groups of proteins shuffle from detergent-soluble to detergent-resistant membrane microdomains during maturation, supporting a model in which the modulation of the phagosome functional properties involves an important reorganization of the phagosome proteome by the coordinated spatial segregation of proteins.
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Affiliation(s)
- Guillaume Goyette
- Département de pathologie et biologie cellulaire, Université de Montréal, and Département de pédiatrie, Centre de recherche de l'hôpital Sainte-Justine, C.P. 6128, Succ centre ville, Montréal, Québec, H3C 3J7, Canada
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47
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Fairn GD, Grinstein S. How nascent phagosomes mature to become phagolysosomes. Trends Immunol 2012; 33:397-405. [DOI: 10.1016/j.it.2012.03.003] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/15/2012] [Accepted: 03/24/2012] [Indexed: 01/18/2023]
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48
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Gómez CP, Tiemi Shio M, Duplay P, Olivier M, Descoteaux A. The protein tyrosine phosphatase SHP-1 regulates phagolysosome biogenesis. THE JOURNAL OF IMMUNOLOGY 2012; 189:2203-10. [PMID: 22826316 DOI: 10.4049/jimmunol.1103021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The process of phagocytosis and phagosome maturation involves the recruitment of effector proteins that participate in phagosome formation and in the acidification and/or fusion with various endocytic vesicles. In the current study, we investigated the role of the Src homology region 2 domain-containing phosphatase 1 (SHP-1) in phagolysosome biogenesis. To this end, we used immortalized bone marrow macrophages derived from SHP-1-deficient motheaten mice and their wild-type littermates. We found that SHP-1 is recruited early and remains present on phagosomes for up to 4 h postphagocytosis. Using confocal immunofluorescence microscopy and Western blot analyses on purified phagosome extracts, we observed an impaired recruitment of lysosomal-associated membrane protein 1 in SHP-1-deficient macrophages. Moreover, Western blot analyses revealed that whereas the 51-kDa procathepsin D is recruited to phagosomes, it is not processed into the 46-kDa cathepsin D in the absence of SHP-1, suggesting a defect in acidification. Using the lysosomotropic agent LysoTracker as an indicator of phagosomal pH, we obtained evidence that in the absence of SHP-1, phagosome acidification was impaired. Taken together, these results are consistent with a role for SHP-1 in the regulation of signaling or membrane fusion events involved in phagolysosome biogenesis.
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Affiliation(s)
- Carolina P Gómez
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, Quebec H7V 1B7, Canada
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49
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Seixas E, Ramalho JS, Mota LJ, Barral DC, Seabra MC. Bacteria and protozoa differentially modulate the expression of Rab proteins. PLoS One 2012; 7:e39858. [PMID: 22911692 PMCID: PMC3401185 DOI: 10.1371/journal.pone.0039858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 05/28/2012] [Indexed: 11/26/2022] Open
Abstract
Phagocytic cells represent an important line of innate defense against microorganisms. Uptake of microorganisms by these cells involves the formation of a phagosome that matures by fusing with endocytic compartments, resulting in killing of the enclosed microbe. Small GTPases of the Rab family are key regulators of vesicular trafficking in the endocytic pathway. Intracellular pathogens can interfere with the function of these proteins in order to subvert host immune responses. However, it is unknown if this subversion can be achieved through the modulation of Rab gene expression. We compared the expression level of 23 distinct Rab GTPases in mouse macrophages after infection with the protozoan Plasmodium berghei, and the bacteria Escherichia coli and Salmonella enterica. We found that P. berghei induces an increase in the expression of a different set of Rab genes than E. coli and S. enterica, which behaved similarly. Strikingly, when one of the Rab proteins whose expression was increased by P. berghei, namely Rab14, was silenced, we observed a significant increase in the phagocytosis of P. berghei, whereas Rab14 overexpression led to a decrease in phagocytosis. This suggests that the parasite might induce the increase of Rab14 expression for its own advantage. Similarly, when Rab9a, whose expression was increased by E. coli and S. enterica, was silenced, we observed an increase in the phagocytosis of both bacterial species, whereas Rab9a overexpression caused a reduction in phagocytosis. This further suggests that the modulation of Rab gene expression could represent a mechanism of immune evasion. Thus, our study analyzes the modulation of Rab gene expression induced by bacteria and protozoa and suggests that this modulation could be necessary for the success of microbial infection.
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Affiliation(s)
- Elsa Seixas
- CEDOC, Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - José S. Ramalho
- CEDOC, Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Luís J. Mota
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Duarte C. Barral
- CEDOC, Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail: (MCS); (DCB)
| | - Miguel C. Seabra
- CEDOC, Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (MCS); (DCB)
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50
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Pei G, Bronietzki M, Gutierrez MG. Immune regulation of Rab proteins expression and intracellular transport. J Leukoc Biol 2012; 92:41-50. [DOI: 10.1189/jlb.0212076] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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